The pathogenic Neisseria are obligate human pathogens that rely on several antigenic variation systems to continually colonize and cause disease in the human population. This proposal will further our studies into the molecular mechanisms used to allow pilin antigenic variation in Neisseria gonorrhoeae. High frequency changes in the pilin amino acid sequence are mediated by gene conversion reactions between one of 18 silent pilin copies and the single expressed pilin gene. In the past funding period, we have identified most of the proteins involved in this process and have demonstrated that the pathogenic Neisseria carry diploid chromosomes that may facilitate gene conversion. We have additionally shown that both the formation of an alternative DNA structure called a guanine quartet (G4), and the transcription of a small RNA within the G4 are required for pilin antigenic variation. In the next funding period we will determine the role of G4 transcription during pilin antigenic variation. Proteins that bind the G4 structure will be identified and we will test whethe these proteins stimulate G4 structure formation or dissolution, and/or the process of pilin antigenic variation. We will also determine whether the G4 structure acts to promote recombination by blocking DNA replication and whether specific helicases prevent a replication stall. We will probe for formation of the G4 structure within the bacterial chromosome and determine whether the G4 structure associates with other DNA sequences. Finally, the effect of various partial loss-of-function mutations on pilin antigenic variation will be determined. The results of these innovative studies will have great impact on the study of Neisserial pathogenesis, mechanisms of antigenic variation, DNA recombination and replication, and the role of alternative DNA structures on molecular processes in many cell types.